Gordon, the M values for the Rquantile normalization are incorrect, the code is currently calculating M as M = M - E = (R - G ) - (qR - R) - qR is quantile normalized R channel, R and G are log channel intensities = 2R -G -qR Quick fix is to change the sign on line 61 of the code chunk : Rquantile = { R <- object$A + object$M/2 E <- normalizeQuantiles(R, ...) - R object$M <- object$M - E # wrong sign object$A <- object$A + E/2 } to Rquantile = { R <- object$A + object$M/2 E <- normalizeQuantiles(R, ...) - R object$M <- object$M + E # sign change object$A <- object$A + E/2 } then M = qR - G, A = (qR+G)/2. > packageDescription("limma", field="Version") [1] "1.8.12" marcus ______________________________________________________ The contents of this e-mail are privileged and/or confidenti...{{dropped}}